Contacts of the helix formed by residues 208 - 212 (chain A) in PDB entry 1U1H
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A TRP* 4.3 7.9 - - + -
113A PHE* 3.4 33.0 - - + -
156A VAL* 5.5 1.3 - - + -
160A SER* 3.7 8.1 - - - +
164A LEU* 5.3 1.1 - - + -
206A ASP* 3.2 18.2 - - + +
207A GLU* 1.3 90.4 - - - +
209A VAL* 1.3 62.3 + - - +
211A VAL* 2.9 29.5 + - - +
241A GLU 3.9 3.8 - - - +
242A THR* 4.6 1.1 - - - -
243A TYR* 3.5 45.8 - - + +
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PHE* 4.2 8.7 - - + -
160A SER* 3.3 37.9 + - - +
163A LEU* 3.5 35.4 - - + -
164A LEU* 4.2 13.9 - - + -
207A GLU 3.0 1.2 + - - -
208A PRO* 1.3 77.5 - - - +
210A LEU* 1.3 52.9 + - - +
212A MSE 2.7 40.7 + - + +
214A LEU* 3.6 20.3 - - + +
222A PHE* 4.5 2.2 - - + -
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A GLU* 3.0 30.0 + - + +
208A PRO 3.0 1.0 - - - -
209A VAL* 1.3 77.7 - - - +
211A VAL* 1.3 59.2 + - - +
212A MSE 3.2 4.1 + - - +
214A LEU* 4.3 3.3 - - - +
219A LEU* 4.0 17.7 - - + -
222A PHE* 3.4 46.2 - - + -
240A VAL* 4.5 2.5 - - + -
242A THR* 4.3 9.9 - - - +
247A ILE* 4.2 8.0 - - + +
248A PRO* 3.6 15.6 - - - +
251A ALA* 3.7 18.7 - - + +
254A THR* 5.3 2.9 - - + -
255A LEU* 3.8 37.0 - - + -
258A LEU* 5.1 2.5 - - + -
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PHE* 4.5 2.7 - - + -
208A PRO 2.9 23.8 + - - +
209A VAL 2.9 0.4 + - - -
210A LEU* 1.3 76.9 - - - +
212A MSE 1.3 78.6 + - + +
242A THR* 3.2 35.7 - - + +
243A TYR 3.5 25.1 - - - +
245A ALA* 3.7 15.8 - - + +
246A ASP 3.9 13.9 - - - +
247A ILE* 4.5 1.8 - - + +
248A PRO* 4.2 0.7 - - - -
615A LEU* 4.1 6.3 - - + -
616A ARG* 2.5 33.2 + - - -
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Residues in contact with MSE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PHE* 4.1 13.2 - - + -
209A VAL* 2.7 32.9 + - + +
210A LEU 3.7 4.5 - - - +
211A VAL* 1.3 114.2 - - + +
213A ASP* 1.3 62.1 + - - +
214A LEU* 3.2 20.7 + - + +
248A PRO* 3.6 12.8 - - - +
615A LEU* 3.1 55.4 - - + +
616A ARG* 3.4 6.1 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il